title: Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/pyrrole-containing polyamides.
abstract: With the aim of incorporating a recognition element that acts as a fluorescent probe upon binding to DNA, three novel pyrrole (P) and imidazole (I)-containing polyamides were synthesized. The compounds contain a p-anisylbenzimidazolecarboxamido (Hx) moiety attached to a PP, IP, or PI unit, giving compounds HxPP (2), HxIP (3), and HxPI (4), respectively. These fluorescent hybrids were tested against their complementary nonfluorescent, non-formamido tetraamide counterparts, namely, PPPP (5), PPIP (6), and PPPI (7) (cognate sequences 5'-AAATTT-3', 5'-ATCGAT-3', and 5'-ACATGT-3', respectively). The binding affinities for both series of polyamides for their cognate and noncognate sequences were ascertained by surface plasmon resonance (SPR) studies, which revealed that the Hx-containing polyamides gave binding constants in the 10(6) M(-1) range while little binding was observed for the noncognates. The binding data were further compared to the corresponding and previously reported formamido-triamides f-PPP (8), f-PIP (9), and f-PPI (10). DNase I footprinting studies provided additional evidence that the Hx moiety behaved similarly to two consecutive pyrroles (PP found in 5-7), which also behaved like a formamido-pyrrole (f-P) unit found in distamycin and many formamido-triamides, including 8-10. The biophysical characterization of polyamides 2-7 on their binding to the abovementioned DNA sequences was determined using thermal melts (ΔT(M)), circular dichroism (CD), and isothermal titration calorimetry (ITC) studies. Density functional calculations (B3LYP) provided a theoretical framework that explains the similarity between PP and Hx on the basis of molecular electrostatic surfaces and dipole moments. Furthermore, emission studies on polyamides 2 and 3 showed that upon excitation at 322 nm binding to their respective cognate sequences resulted in an increase in fluorescence at 370 nm. These low molecular weight polyamides show promise for use as probes for monitoring DNA recognition processes in cells.
authors.affiliation: Division of Natural and Applied Sciences, Department of Chemistry, Hope College, Holland, Michigan 49423, United States.
authors.forename: Sameer
authors.initials: S
authors.lastname: Chavda
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.forename: Balaji
authors.initials: B
authors.lastname: Babu
authors.forename: Ryan
authors.initials: R
authors.lastname: Davis
authors.forename: Alan
authors.initials: A
authors.lastname: Sielaff
authors.forename: Jennifer
authors.initials: J
authors.lastname: Ruprich
authors.forename: Laura
authors.initials: L
authors.lastname: Westrate
authors.forename: Christopher
authors.initials: C
authors.lastname: Tronrud
authors.forename: Amanda
authors.initials: A
authors.lastname: Ferguson
authors.forename: Andrew
authors.initials: A
authors.lastname: Franks
authors.forename: Samuel
authors.initials: S
authors.lastname: Tzou
authors.forename: Chandler
authors.initials: C
authors.lastname: Adkins
authors.forename: Toni
authors.initials: T
authors.lastname: Rice
authors.forename: Hilary
authors.initials: H
authors.lastname: Mackay
authors.forename: Jerome
authors.initials: J
authors.lastname: Kluza
authors.forename: Sharjeel A
authors.initials: SA
authors.lastname: Tahir
authors.forename: Shicai
authors.initials: S
authors.lastname: Lin
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Kiakos
authors.forename: Chrystal D
authors.initials: CD
authors.lastname: Bruce
authors.forename: W David
authors.initials: WD
authors.lastname: Wilson
authors.forename: John A
authors.initials: JA
authors.lastname: Hartley
authors.forename: Moses
authors.initials: M
authors.lastname: Lee
mesh_terms: D001483:Base Sequence; D002151:Calorimetry; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D003850:Deoxyribonuclease I / Q000378:metabolism; D015195:Drug Design; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000737:chemistry / Q000378:metabolism; D007093:Imidazoles / Q000737:chemistry*; D008836:Micrococcal Nuclease / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009757:Nylons / Q000138:chemical synthesis / Q000737:chemistry* / Q000378:metabolism*; D011758:Pyrroles / Q000737:chemistry*; D013050:Spectrometry, Fluorescence; D013379:Substrate Specificity; D020349:Surface Plasmon Resonance
chemical_list: D005456:Fluorescent Dyes; D007093:Imidazoles; D009757:Nylons; D011758:Pyrroles; C029899:imidazole; D004247:DNA; D003850:Deoxyribonuclease I; D008836:Micrococcal Nuclease